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You can use VariantFiltration to apply new filters to sites that you have in your VCF (which is roughly the equivalent of changing --stand_call_conf), but you can't do the equivalent of changing --stand_emit_conf.

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You can use VariantFiltration to apply new filters to sites that you have in your VCF (which is roughly the equivalent of changing --stand_call_conf), but you can't do the equivalent of changing --stand_emit_conf.